# Empowering Heterogeneous Graph Foundation Models via Decoupled Relation Alignment

arXiv: https://arxiv.org/abs/2605.00731 · HTML: https://mlsanity.com/paper/2605.00731/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 33 of its 49 references that are in the map.
- First posted on arXiv 1 May 2026.

## Builds on (most cited first, 30 of 33)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Heterogeneous Graph Attention Network](https://mlsanity.com/paper/1903.07293/) (2019)
- [Heterogeneous Graph Transformer](https://mlsanity.com/paper/2003.01332/) (2020)
- [Graph Neural Networks in Recommender Systems: A Survey](https://mlsanity.com/paper/2011.02260/) (2020)
- [Meta-Learning for Semi-Supervised Few-Shot Classification](https://mlsanity.com/paper/1803.00676/) (2018)
- [MAGNN: Metapath Aggregated Graph Neural Network for Heterogeneous Graph Embedding](https://mlsanity.com/paper/2002.01680/) (2020)
- [Progressive Feature Alignment for Unsupervised Domain Adaptation](https://mlsanity.com/paper/1811.08585/) (2018)
- [Graph neural networks for materials science and chemistry](https://mlsanity.com/paper/2208.09481/) (2022)
- [GraphPrompt: Unifying Pre-Training and Downstream Tasks for Graph Neural Networks](https://mlsanity.com/paper/2302.08043/) (2023)
- [Self-supervised Heterogeneous Graph Neural Network with Co-contrastive Learning](https://mlsanity.com/paper/2105.09111/) (2021)
- [Graph Foundation Models: Concepts, Opportunities and Challenges](https://mlsanity.com/paper/2310.11829/) (2023)
- [Universal Prompt Tuning for Graph Neural Networks](https://mlsanity.com/paper/2209.15240/) (2022)
- [Unsupervised Attributed Multiplex Network Embedding](https://mlsanity.com/paper/1911.06750/) (2019)
- [All in One and One for All: A Simple yet Effective Method towards Cross-domain Graph Pretraining](https://mlsanity.com/paper/2402.09834/) (2024)
- [HDMI: High-order Deep Multiplex Infomax](https://mlsanity.com/paper/2102.07810/) (2021)
- [SAMGPT: Text-free Graph Foundation Model for Multi-domain Pre-training and Cross-domain Adaptation](https://mlsanity.com/paper/2502.05424/) (2025)
- [Interpretable and Efficient Heterogeneous Graph Convolutional Network](https://mlsanity.com/paper/2005.13183/) (2020)
- [Heterogeneous Graph Masked Autoencoders](https://mlsanity.com/paper/2208.09957/) (2022)
- [Domain Adversarial Neural Networks for Domain Generalization: When It Works and How to Improve](https://mlsanity.com/paper/2102.03924/) (2021)
- [HGPROMPT: Bridging Homogeneous and Heterogeneous Graphs for Few-shot Prompt Learning](https://mlsanity.com/paper/2312.01878/) (2023)
- [Text-Free Multi-domain Graph Pre-training: Toward Graph Foundation Models](https://mlsanity.com/paper/2405.13934/) (2024)
- [Multi-Domain Graph Foundation Models: Robust Knowledge Transfer via Topology Alignment](https://mlsanity.com/paper/2502.02017/) (2025)
- [HetGPT: Harnessing the Power of Prompt Tuning in Pre-Trained Heterogeneous Graph Neural Networks](https://mlsanity.com/paper/2310.15318/) (2023)
- [Self-supervised Heterogeneous Graph Pre-training Based on Structural Clustering](https://mlsanity.com/paper/2210.10462/) (2022)
- [Edge Prompt Tuning for Graph Neural Networks](https://mlsanity.com/paper/2503.00750/) (2025)
- [GRAVER: Generative Graph Vocabularies for Robust Graph Foundation Models Fine-tuning](https://mlsanity.com/paper/2511.05592/) (2025)
- [Revisiting Self-Supervised Heterogeneous Graph Learning from Spectral Clustering Perspective](https://mlsanity.com/paper/2412.00742/) (2024)
- [SA2GFM: Enhancing Robust Graph Foundation Models with Structure-Aware Semantic Augmentation](https://mlsanity.com/paper/2512.07857/) (2025)
- [MUG: Meta-path-aware Universal Heterogeneous Graph Pre-Training](https://mlsanity.com/paper/2602.22645/) (2026)

## Built on by (most cited first, 1 of 1)

- [Cascade-KDE: Robust Time-Series Restoration under Out-of-Distribution Impulse Corruptions](https://mlsanity.com/paper/2605.24055/) (2026)

## Abstract (arXiv)

While Graph Foundation Models (GFMs) have achieved remarkable success in homogeneous graphs, extending them to multi-domain heterogeneous graphs (MDHGs) remains a formidable challenge due to cross-type feature shifts and intra-domain relation gaps. Existing global feature alignment methods (PCA or SVD) enforce a shared feature space blindly, which distorts type-specific semantics and disrupts original topologies, inevitably leading to "Type Collapse" and "Relation Confusion". To address these fundamental limitations, we propose Decoupled relation Subspace Alignment (DRSA), a novel, plug-and-play relation-driven alignment framework. DRSA fundamentally shifts the paradigm by decoupling feature semantics from relation structures. Specifically, it introduces a dual-relation subspace projection mechanism to coordinate cross-type interactions within a shared low-rank relation subspace explicitly. Furthermore, a feature-structure decoupled representation is designed to decompose aligned features into a semantic projection component and a structural residual term, adaptively absorbing intra-domain variations. Optimized via a stable alternating minimization strategy based on Block Coordinate Descent, DRSA constructs a well-calibrated, structure-aware latent space. Extensive experiments on multiple real-world benchmark datasets demonstrate that DRSA can be seamlessly integrated as a universal preprocessing module, significantly and consistently enhancing the cross-domain and few-shot knowledge transfer capabilities of state-of-the-art GFMs. The code is available at: https://github.com/zhengziyu77/DSRA.